The top general in Afghanistan has a friendly-fire incident.

Last week Gen. David Petraeus collapsed. This week Gen. Stanley McChrystal did. The top commander in Afghanistan and his team were the subject of a profile in Rolling Stone in which they looked petty, frustrated, and reckless. President Obama and his staff now must evaluate whether to relieve McChrystal of his command.

You're never supposed to surprise your boss. The story not only surprised Obama, it presented him with a new problem when he's already facing a few. Yet unlike his most recent problem—the Gulf spill, where he's limited by what he can do—on this issue, the president has total control. He has two decisions to make. The first is about McChrystal's future. The second is about the strategy in Afghanistan. Whatever the president decides about McChrystal, he will have to explain it in the context of the strategy in Afghanistan. As a Pentagon official has said, "McChrystal is the Afghanistan strategy."

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In the article McChrystal himself says Obama was unprepared in their first meeting and makes fun of Vice President Joe Biden as well as Richard Holbrooke, the administration's special envoy to Pakistan and Afghanistan. He also appears to knock the current Ambassador to Afghanistan Karl Eikenberry. And the quotes from his aides are worse. The general view of his team seems to be that they know best and Washington is clueless; one aide calls White House National Security Adviser James Jones a "clown."

Granted, this is the kind of trash talking that goes on every day in private and particularly around men trained to be ferocious and fight wars. These guys were just dumb enough to do it in front of a reporter, and in some cases it appears as though this talk occurred in McChrystal's presence. He's responsible for his team, and they wouldn't speak so freely if they thought the boss believed something else. But the fact that McChrystal himself does not seem to have said anything insubordinate may be the deciding factor in how the president treats him now. Also, a lot of the material is also about personalities and behavior, not the policy in Afghanistan.

McChrystal responded to the story by calling Vice President Biden and others involved. He did not speak with the president but offered an apology. "Throughout my career, I have lived by the principles of personal honor and professional integrity," he said. "What is reflected in this article falls far short of that standard." He will have a chance to offer it in person. Obama has called him back to join Wednesday's regularly scheduled meeting about the war.

What's does McChrystal actually think about the president? There's a high degree of frustration with the administration obvious in the Rolling Stone article, but it doesn't come across that McChrystal thinks Obama doesn't know what he's doing. In conversations I had with sources involved in the military side of the Afghanistan-Pakistan review at the end of last year, McChrystal was described as feeling very positive about how the president handled the process. (He wasn't positive about everyone in the administration.) Obama was described as in command of the process, playing an honest broker in the battle between the various factions.

Obama isn't the only boss McChrystal has irritated. He's also ticked off Defense Secretary Robert Gates. Gates, as a general matter, hates this kind of talking out of school. It reflects badly on the mission if the person leading it shows this lack of judgment. Also, McChrystal was Gates' handpicked general. And internally, it puts the Pentagon on the defensive in the intramural battles with the White House. Reports are that Obama is "furious." What House aides were already chafing at pressure they were getting from the military to soften the terms of the planned withdrawal of troops from Afghanistan in July.

A lot of people have been calling lately for Obama to get angry. (If only Tony Hayward's aides had said stupid things to Rolling Stone.) Congressman David Obey, a fierce war critic, has called for Obama to fire McChrystal. But this is probably a case in which the country needs the calm, unemotional Obama. This particular Rolling Stone story, and the months-long fracas between the White House and Pentagon over Afghanistan strategy, already has too much testosterone. If for no other reason than to bring the humors in alignment, there needs to be a force for restraint.

There are a lot of reasons for the president to overreact. He has to send a message—to his military, to foreign leaders, and to political opponents—that reaffirms the general principle of civilian control of the military and his control of the Pentagon in particular. There's also a cheap public relations reason to slap McChrystal extra hard. Given the criticism Obama has received for not showing command in the Gulf, he could presumably use this opportunity to look tough.

At the same time, it's important to see this controversy in context, and that argues for restraint. The article is an outgrowth of a skirmish that has been going on since the Afghanistan policy review started last year. Obama made his policy choice in December—essentially, send more troops but with a clear date in July 2011 for withdrawal—but the battle has continued behind the scenes. One recent battle concerned Jonathan Alter's account of the policy review in his book, which Pentagon officials read as a score-settling by those in the administration who felt the military had tried to roll them. The president has to send the clear message: enough.

But the main reason the president has to show restraint is that he can't let the controversy become a proxy for undoing the Afghanistan policy he still supports. He has to rap McChrystal on the knuckles but turn the message back to the mission—the war in Afghanistan is at a very tough point. Violence is increasing, and this year may be one of the deadliest years for American troops. Progress has been slow. Unless Obama has problems with McChrystal's performance, and there's no evidence that he does, McChrystal's remarks are beside the point. McChrystal will have to go back to Afghanistan and carry out Obama's mission, and he can't do that from a weakened position. That's true not just with his own troops, but with leaders in Afghanistan. If the administration posture is really to be more accommodating of President Karzai then getting rid of McChrystal makes no sense. He's the administration's best asset with the Afghan president.

Everyone I talk to, both inside and outside Washington culture, wants to know: Why would McChrystal (or his aides) say such things? One Pentagon source says the volcanic ash is to blame. The reporter was supposed to have limited time with McChrystal. When the ash hit, the general and his team were stuck. The reporter essentially became embedded. The military men forgot they had a reporter near and expressed sentiments that are very close to the top (sometimes because they were drunk).

The most damaging part of the article, from a policy perspective, is its description of the counterinsurgency strategy. This is the central theory behind both the Iraq and Afghanistan conflicts. Petraeus used to be the face of the counterinsurgency doctrine—calm, learned, steady. McChrystal was thought to be in his mold. If this article becomes gospel, there's a chance that the reckless McChrystal becomes the new face of the strategy. This will make it harder for proponents to argue for the strategy in the future if for no other reason than it distracts from signs of progress.

The second half of the article suggests that the strategy has been a failure because the troops asked to carry out the theory don't buy it. This is one of the key challenges and tensions of counterinsurgency warfare, as Marine Gen. James Mattis explained when I talked to him earlier this year. But the tension between assuming more physical risk and using less force in the hopes of winning over the population is not a new tension. It's a part of the strategy and complexity that Obama signed onto after months of review.

Still, that doesn't mean that Obama welcomes the chance to reiterate his strategic rationale. This controversy will kidnap the White House agenda. Today's message was supposed to be about health care, and in his remarks the president was distracted by a fly. He shooed it away, joking that the last time that had happened he'd dispatched the fly completely. This McChrystal story is a much bigger distraction and will require much more careful handling.